


The Matrix Rebellion

by Madzie2000



Category: The Matrix (Movies)
Genre: Sequel, The year is 2216 (2016)
Language: English
Status: In-Progress
Published: 2016-02-23
Updated: 2016-09-07
Packaged: 2018-05-22 19:33:50
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence, Major Character Death
Chapters: 9
Words: 9,882
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6091759
Author URL: https://archiveofourown.org/users/Madzie2000/pseuds/Madzie2000
Summary: <blockquote class="userstuff">
              <p>Neo is brought back from the dead by a teenager called Ezra who has the ability to bend the Matrix to her will in ways that differ in the slightest way from Neo. As their friendship progresses, Neo and Ezra find out more about the abilities they have, their past and the changes that have occurred since Neo's death.</p>
            </blockquote>





	1. Neo's Awakening

Neo was asleep in the Matrix: almost waiting for the time when he would reappear within the code. His mind remembered the feeling of death, cold and lonely, and then something hard and callous against his back brought his awareness from the depths of his sub-conscious mind, letting him feel that code once again. It moved with him, through him, around him, as it once had. Neo was no longer dead, but alive, laid out on the gravelly earth within the Matrix, his eyes opening to see a purple sky stretching out above him in a meagre welcome. The code was different, lighter without the heavy presence of Agent Smith, yet he could feel eyes on him, watching and waiting, but for what purpose? He sat up and looked around, taking in every sight as his eyes scanned for somebody lurking in the early-morning shadows. Their feet moved swiftly yet silently through the faintest awareness of his conscious mind, hiding where he couldn’t quite see. The piles of metal to his left were scraps, twisted or faulty machinery that had been boxed up by a trash compactor he could hear in the distance. The diamond mesh fences were tall and topped with razor-wire to keep out scavengers, a practice befitting a junkyard.

_Full of the useless junk within the Matrix… old files, unused data, I suppose I’ll find Smith in here somewhere._ Neo walked onward past crushed cars, noting their age and the way they differed only in the slightest of ways, as if the Matrix recognised its own faults and destroyed them to keep order within the programming. It had always been trial and error as that crazy, blonde-haired boy Mouse had said: they don’t know about the taste of food. They have to search around for the information and copy it to the best of their abilities, being applied to everything from vehicles to infrastructure. _He was right… I hope he didn’t die in vain. If I’m alive inside the Matrix, something must be wrong. My time is limited for sure; Morpheus said it himself. “The body cannot live without the mind”._ Neo let his concealed sadness die down, his fist unclenching as he relaxed. He didn’t even know if Morpheus was still alive. The person in the shadows was still following him, nearly silent as their feet patted against the metal stacked high around him. Neo finally stopped by a pile of metal beams, realising that it was old framework of some kind, worn and rusted to dark shades of amber. Lightning began to streak the sky, the bright light casting shadows in all directions, toying with his mind. Neo thought he saw something move in his peripheral vision, so he spun on his heels.

 

Standing atop boxed up, compacted metal was the silhouette of a woman: broad shoulders making her seem far more masculine. Her clothing had been hidden by the flash of lightning behind her, but the flash dissipated, revealing the usual black regalia of those who’d been released from the Matrix.

However, this woman dressed similarly to Trinity, no capes, cloaks or trench-coats flowing out to the sides. Instead, she was clad in black boots with a light heel, pants made of black leather and a jacket made of the same material that only stretched to her midriff. The rest of her stomach was hidden by a black shirt. Her face was invisible behind the motorcycle helmet she wore, the tint on it so heavy that he couldn’t see any of her defining features.

“Who are you? Why am I here?” Neo heard a deep, masculine voice come from the helmet and he knew immediately that the dial he had spotted earlier was some kind of voice modulator.

“Don’t patronise me Neo. I am the one who brought you here and I could easily put you back where you came from. We will ask questions later, when the time is right. I will take you to the underground base where I and the others hide from the threat you believed to have destroyed 16 years ago.”

Neo was inwardly excited, knowing it was possible that Morpheus and the others were alive, though they would be older than he remembered them to be. His thoughts were cut off by a realisation that rocked him to the core.

“Smith is alive?” The woman nodded once, giving a small gesture to a pile of metal at her left, just past where he was standing.

“Would you like to leave? Pick up a piece and give it to me.” Neo picked out a piece of scrap that had fallen out of a compressed cube, ripping it off and cutting his hand across the palm.

“Ah!” The woman shook her head in mild amusement, surprised that Neo was so careless.

“Being over-eager doesn’t help anybody, especially you.” She moved closer to Neo and he hesitated, unsure of what she was going to do.

“Give me the scrap first.” Neo bent down and picked up the metal from the ground, putting it in the woman’s outstretched hand. She pulled her jacket to one side and shoved the metal inside, revealing more scrap metal and a single handgun. Using the opportunity he had, Neo grabbed the helmet on both sides - despite the pain searing his palms – and ripped it form her head, throwing it to the ground, putting a web-like crack across the visor.

 

The woman’s hair flew around her face, barely concealing the anger she had building up in her veins. She looked at Neo, eye to eye, and he felt his heart sink. It hadn’t been an Agent in disguise as he’d assumed: instead he saw the features of a teenage girl, her aggression more than obvious. The naturally deep tone in her voice was nowhere near as powerful as the voice modulator, but it still shone through as she spoke.

“What was that for? I try to heal your wounds and you reveal my identity before I have time to give an introduction? That’s a little rude, isn’t it?” The girl gave him a questioning, sarcastic smile.

“By heal you mean fix this?” Neo put out his hand and the girl could see hesitation in his body language, reluctance to let a stranger, in the Matrix of all places, do something he had never seen before. The smile lost its sarcastic nature, almost disappearing completely as she put a hand under Neo’s. She stepped closer to better inspect it, analysing the code and noting the pain threshold of male humans in their late 20’s.

“This will hurt you, but not as badly as it could have. A few millimetres deeper and this would be infected.”

Neo watched the girl’s other hand sit on top of the gash, holding back the urge to wrench his hand away. Though he found it odd to have someone take this much interest in him, he had to see this healing process for himself. The girl pushed her hands together lightly and Neo winced, the pain quickly subsiding. In a flash of green light, the pain hit a sudden high and he jerked out of the girl’s grasp. All Neo could do was stare at his hand as code rushed to his wound and healed it, closing the flesh over and sterilising the red patch that indicated a light infection. The girl was glaring at Neo, noticing that he was beyond shocked by her abilities.

“How did you do that?” The girl froze, trying to put her words together carefully, knowing that a few words in the wrong arrangement could lead to her death at the hands on The One.

“Would it be okay if I start with my name?” Neo could have slapped himself across the face. _Why **didn’t** I ask you your name first instead of being reckless?_ He nodded, still feeling a little guilty.

“My name is Ezra. I know your name, Neo. Everybody at the base does.”

 

 

This is the re-make of my old fic of the same name with the same storyline and I hope it meets your reading needs! Next chapter will be out sometime next week or earlier if I can :)


	2. Leaving the Junkyard

**Summary for the Chapter:**

> Neo knows who his new companion is, but so many questions remain...

“Where is the base?” Ezra kept her expressions neutral so Neo could only read her body language, the slight breeze making her elbow-length hair flow around her face like the waves of an ocean. He found himself staring at the code, the way it twisted within the micro-thin fibres of each hairs, sending them in different directions.

“Not too far from here, underground where Smith will never find it… not completely.” Neo didn’t like it when he was forced to guess what everybody meant in the Matrix.

“Answer me two questions and I won’t annoy you with any more.”

“Agreed. The first?” Neo kept his eyes on Ezra as she took the metal back out of her jacket.

“Are you a program sent to destroy me?” Ezra gave a high-pitched chuckle that reminded him of a hyena, a smile coming over her.

“And what would that do for us? Leave us with no hope for a saviour perhaps? Killing you would be a waste of time because I am on **your** side, not his. You would just go back from the place you’d been for 15 years.”

“Where was I?”

“Do you really want to know the answer or would you prefer to ask another question?”

 

Neo looked down at the scrap in Ezra’s hand and knew she was right.

“How could Smith not completely know where you are: he either does or he doesn’t.” Ezra nodded once at the question as if she knew it was a better choice than any other he could have chosen.

“A wise choice. The underground base is hidden from prying eyes and can only be opened by those with the ability to bend the code of the Matrix like us. So far in my 15 years I have found 150 orphans and taught them everything I know, taking them away from the cruelties that the Matrix hides. I consider myself to be their caretaker.”

“When do we leave?”

“Now. On this.” Ezra held the scrap metal in her hands up for Neo to see. She walked out to an open area of the junkyard and carefully sat the metal on the ground, stepping back as Neo came closer to her. The metal gave off a green glow and its code appeared, forming blocks and then curved shapes in the air, gaps filled by luminescent, translucent code that was too small to see. When the code disappeared, a motorbike was left in place of the metal and Neo held back the urge to ask what had happened. It was obvious: she had forced the metal’s code to change, multiply, expand and form into the shape of a motorcycle so they could leave the junkyard without other vehicles getting in the way.

 

Ezra sat on the motorbike and patted the seat behind her with a small smile, kicking up the stand so that she kept the motorbike standing still. Neo hated to admit it, but he secretly loved motorcycles, the way adrenaline would rush through his body as the wind swam over his face and hair. Ezra could feel how jittery he was; not knowing who she was in a definite sense made it hard, but being worried about invading her personal space was likely the hardest part of all. Neo just wasn’t accustomed to riding a vehicle with two people unless it had four wheels. With a small hint of reluctance, Neo sat behind Ezra and she moved forward so he had room to fit on with her. Neo wrapped his long fingers around the rim of the motorcycle’s seat and Ezra sighed, knowing exactly what he’d done to avoid putting his hands on her.

“Do you plan on losing your fingers?” The venom in her voice let out a small spark of fear in his mind. _And I thought Trinity was scary when she got angry…_ When Neo gave no reply, Ezra grabbed his hands and quickly slammed them into her hips putting her own back onto the handlebars. Neo was in complete awe of her harsh methods of getting him past the barrier of personal space, but he didn't let it show at all. Ezra was annoyed and aimed a rather crude comment in his direction, her head moving to one side of her shoulder as she spoke.

“So innocent.”

 

As Ezra kick-started the bike, they both smirked. _At least she has a sense of humour._ Ezra was also secretly expressing relief, but not in the way Noe was: he was happy that she knew how to have fun, but she was happy that he hadn’t pulled out a gun and shot her for making such an inappropriate jibe. She knew that he had killed, more than likely made love to someone and had definitely seen gore beyond measure: that was why they found it so funny.

“The little things make life worth living.” Ezra revved the motorbike’s engine and they took off through the piles of scrap metal, dodging through them with her seemingly supernatural reflexes. She felt Neo’s hands dig into her ever so slightly and she could feel how alert he was, searching for their target. Neo finally spotted it: a tall, wide tunnel made of a smooth concrete on the other side of the junkyard. The closer they got, the more he realised it had shrunk from the possible 10 metres to a less impressive 4. Neo felt like he needed to duck his head, but he knew he wasn’t **that** tall. They entered the tunnel and immediately the sharp turns had them both moving with the motorbike, fighting with their muscles to prevent a crash. One wrong move could mean serious injury, or even death. Ezra finally straightened up with the tunnel and saw a shadowy figure at the end of the tunnel, their outline so familiar to both that they didn’t even need to take a second glance. Ezra turned the motorbike one way and it skidded to a stop, she and Neo both getting off and staring down the one man Neo had been charged with destroying: Agent Smith.

Nobody has seen this yet but I'm sure the pace will pick up sometime this year(?).


	3. Smith vs The Two Prodigies

**Summary for the Chapter:**

> Ezra and Neo go up against Smith and end up with seems to be a set of bad injuries, but Ezra will do something in front of Neo that could change the way he and the others in Zion think about the Matrix.
> 
> This is probably one of the coolest scenes I've written in terms of action, so if something doesn't make sense feel free to tell me in the comments. Feedback is HIGHLY appreciated! Enjoy your day/night :)

Smith was grinning as Ezra stalked a little closer to him.

“I don’t remember inviting you, old man.” Smith was hiding his rage and gave her a fierce yet cheeky smile that made Ezra and Neo’s blood both curdle and boil. Keeping his face clear of any emotion to stop Smith from using this to his advantage, Neo looked at Ezra and felt like he was vulnerable.

“Do you have a weapon?” Ezra smiled and turned to him, pulling a piece of metal tubing from her jacket in one swift motion.

 

“Of course.” Ezra closed her eyes in concentration, focusing on the metal in her hand. Smith wanted them to think they would be safe, standing and waiting. In only a few seconds, Ezra had created a pole that was at least 4 metres long, the green code rearranging in front of Neo’s eyes. With the effort of breaking a cracker with her fingers, Ezra broke the pole over her knees; one half of the pole she passed to Neo and the other she cracked in half again. Armed and ready to fight, Ezra stepped even closer to Smith, giving her a sense of being powerful. _So eager to take me out… it’s nice to know that somebody thinks of me._ Ezra waited for Smith to make the first move, and he did. As soon as Neo found a comfortable way to grip the pole, Smith charged forward and screamed in ager, using it to fuel his actions. Ezra stepped away from Smith as he ran at her with inhuman speed, a fist raised and ready to punch her. The moment her boot left the ground, Smith swiped his own foot under Ezra and knocked her to the ground.

 

Smith snatched one pole from Ezra and took a swipe at her head, but she rolled in time to dodge it, cracking the cement in a web-like pattern. Using his pole like a baseball bat, Neo swung at Smith, but the ex-agent blocked the hit easily. Neo was about to be impaled by Smith, but Ezra pushed Neo over and he fell onto his back, sitting up on his elbows in time to see something he would never forget. Smith had smashed the pole against Ezra’s skull as she stood up to fight him, sending the girl rolling across the ground. In her jacket, the metal pressed against her body and pierced her chest and stomach. Small rocks and metal scattered over the ground dug into her face, leaving bruises and scratches that Neo couldn’t see. He stood up quickly and tried to hit him in the back, but Smith was faster, using his strength to hit Neo in the stomach, an audible crack coming from him as he hit the tunnel’s wall. Smith dropped the pole as Neo sluggishly opened his eyes, listening to every word Smith had to say.

 

“Humans are pathetic. You wanted to help her because your morals and emotions didn’t let you see what I see. I see how you have ruined your home world with emotion, letting anger take over your very being and allowing it to consume you until you can no longer bear to share the earth with one another. Eradicating you and this girl will be my greatest triumph. You have a month to gather your thoughts, learn of the changes your death created as well as all the problems it started; once you have learned of all the bad you have given birth to, I will attack that useless group of orphans with everything I have.” As Neo let his heavy eyelids fall, Smith walked from the tunnel and found the Freeway a short distance away, assimilating the first program he saw come down long stretch of road. _I’ve always wanted to be in a figure of authority._ Smith smirked in amusement and continued to drive onward. The girl would certainly be after him and he would be ready for her, as he always was.

 

Back in the tunnel, Neo was the first to wake up and he thought of crawling over to Ezra, but an intense, burning and aching sensation in his shin stopped him. Neo had to put a hand over his own mouth to stop the groans coming from it, the pain growing to an almost unbearable degree. Ezra woke up with a start, hearing muffled groans she could, inexplicably, recognise as Neo’s. She was still groggy as she touched a hand to her head, feeling the dent where her skull had been pushed inward. Using a small burst of energy, Ezra healed the broken bone, the pain hitting her as hard as Smith had. Neo winced for two reasons: the first, the pain in his leg wasn’t fading out. The second, an inhuman scream had filled his ears and it could only be one person: Ezra. The girl was holding her head, but he couldn’t figure out why. Memories flooded back into his head and he remembered the hit Smith has scored on her temple. _If he hit her that hard, surely she’d be dead, right?_

Neo watched Ezra stand and turn, her injuries far worse than his own. At least, he thought so. Ezra staggered over to him almost falling into a sitting position by his feet and slowly rolling his pants back so that she could see the broken leg. Neo wanted to stop her, but he had no choice but to sit there as the blood loss had gotten so severe he could barely keep his head up. Ezra’s words were definitely a small comfort, but Neo felt as though she was teasing him.

“I can’t believe everything turned out this way. Do **you** trust **me**?” Neo hadn’t realised that his eyes had closed in response to the blood spilling form his leg, but he managed to open them, looking down at his leg and seeing the damage. A piece of bone was poking through his skin, a stark contrast of white against his pale skin and the bright red blood that was flowing from the wound. Ezra pulled the pant-leg up until it was laid just above his knee, tightening it around his leg to stop more blood from leaving his body. Neo could only moan at the pain, barely staying awake as he watched Ezra stare into his eyes, realising how much they reminded him someone else’s.

 

“You said you trusted me, right? Well… I’m afraid I have to test your honesty.” Ezra put a hand to the concrete ground and Neo wished he could jump away as some of the concrete slithered around his wrists form both sides, feeding upward from the ground, making him think of the tent pegs his father had used when they went camping. The green, glowing concrete snakes met up on the back of his wrists and froze suddenly, stopping his hands from moving. Ezra had her hand pointed at Neo’s arms, then moved them down to his ankles. The concrete here went through the process and, like the ones at his wrists, froze up and left the area around the strange anchors indented. _She rushed everything so much… she forgot to… replace the code._ Neo’s heart was beating slower and slower by the second and Ezra couldn’t figure out why. Realising quickly that she had loosened the grip on the pant-leg, she made the concrete grasp itself around the skin just above his knee where the pants had been and she took a step back.

“This is going to hurt, a lot.”

 

In a second, a mere moment, the pain in Neo’s leg surged and dissipated as quickly as it had come and the lost energy in his body returned. Neo yanked his arms upward and broke the cements bonds, doing the same with his legs. He stood up and towered over Ezra, who backed up when their bodies almost touched, the pair now standing in the centre of the tunnel as rays of light began to enter through the opening on their right.

“Why did you pin me down and evade my privacy like that?” Ezra was clearly mad, but there was a hint of confusion in her eyes. Her voice was stern and threatening and he wanted to laugh. She looked like a young child, a mere two or three years old, who hadn’t gotten what she wanted for Christmas.

 

“Well excuse me for not wanting you to kill me or see you die. Without one of us we can’t destroy Smith. You saw, felt **and** heard what he can do to us when we fight him one on one: he knocks us down one by one. If you learnt to work with me rather than against me, maybe we could have killed him.” Ezra lowered her voice so that Neo wouldn’t hear her own uncertainty.

“So it’s all my fault? What about you, standing ready while I got my bearings? Would you call that teamwork Ezra?” Ezra threw her sarcasm in his face and Neo knew that he deserved it: when he was angry he said all sorts of mean things. In return, Ezra knew he was right, but she just added fuel to the fire of their argument regardless of their calming tempers.

 

“Oh, so I have a name all of a sudden do I Neo? How kind you to use it so often!” In what seemed to be the blink of an eye, Ezra had gotten onto the motorcycle just beyond the bend of the tunnel, a fair walk from where they were by the exit. She started up the motorbike and drove it toward him, speeding up as she got closer. Neo didn’t run: he knew she wouldn’t hit him. When she slowed and suddenly stopped, he waited, thinking critically about her methods of letting off steam. _So you could have done something else but decided that nearly running me over was the best option? You really are a teenager; reckless._

 

“Come on Grumpy, get on before I run you over for real.” Neo noticed how Ezra’s personality had changed, pinning it down to mood swings that would generally occur in children her age. God knows he had a lot of those in his youth. Neo walked around the back and looked down to his leg, secretly amazed. There was no trace of injury anywhere to be seen. He bent over and pulled the pant-leg back down where it should be and swung his good leg over the motorbike, the previously hurt one still on the ground, waiting for Ezra to tell him he could grab onto her. As if giving him a reply, Ezra turned her head, letting Neo hear her a little more clearly.

 

“Ready?” Neo lightly placed his hands back on her hips, expecting her to snap, but instead she revved the engine twice, making sure Neo had enough warning to hold on. His grip on her tightened a little more and she finally drove out of the tunnels exit, stopping the motorbike on a hill made mostly of dirt, with patches of grass hiding here and there. Down one side of the hill to their right was a large complex, full of houses, the homes of programs and entrapped humans. A thought in the back of Neo’s mind came forward and was begging to be answered: he hated long explanations but they were the only ones that would make sense in the Matrix.

“Why did we stop? Don’t you need to get back to all those orphans?”

 

Okay, Chapter 4 won’t be out until Wednesday next week unless I see a definite need for another, so be patient (if you can)!      


	4. The Guessing Games

**Summary for the Chapter:**

> Ezra gives Neo an answer to his question, but it only leads to more. What will Neo hear that he doesn't expect?

“I know that they’re more than capable of keeping themselves safe. Look at the sunrise and tell me what you see.” Neo’s eyes darted from Ezra’s turned head to the sun directly in front of them, wishing he could reach out and touch the magnificent colours before him, layering up through to white, fluffy clouds. _It’s so…_ He fell silent, taking in the sight before him.

“It’s beautiful.” Ezra grinned.

“Somebody made that for you when they were a little girl; now they’re all grown up and living better than they ever could have, had you not crossed their path.”

“You?” Ezra laughed, driving the motorbike down the small hill onto a small stretch of road, going slowly as they made their rode toward the Freeway.

“No. Sadly, I was born shortly before your death, so you had no effect on my life. At least, not that I know of.”

 

Neo gave a small grin and Ezra could feel the shift in his body’s code, a slight shift upward in his facial muscles. The older man's mind was shifting, thinking hard. Then he realised that there was only one other 'little girl' he had met in his life as The One.

“Sati made that? For me?” As they got onto the Freeway, Ezra turned her head, both checking behind her and looking at Neo.

“Answer me this: how could she have changed the code in the Matrix to form something as intricate as a dishevelled rainbow in the sky? The last time you saw her she was a ten-year-old girl looking for a place to live and suddenly she can manipulate the code like me, but how?” Ezra loved letting people guess. Sometimes the wrong answer was the funniest or they got it the first time around, which would leave her bored. Neo was going to be one of those people that left her bored, **constantly**. Ezra's eyes were back on the dark cement of the road, dodging carefully between cars and checking the speedometer with a strange carefulness. 

 

“Sati took the place of the Oracle?” The disbelief in Neo’s voice made it hard for Ezra to stop her now-constant smile.

“Now she **is** the Oracle and her predecessor gave me one wish that could only be granted to me while I was inside the Matrix. A parting gift, if you will.”

“What did you wish for?” Ezra sighed.

“That’s a little harder to explain without seeing you face to face. I’m sure you can wait twenty minutes or so.”

“When did you last see her?” _Now **that**  I can answer._

“Thankyou. About a week if memory serves. I told her of my plans to bring you back and she agreed on one condition.” Neo said nothing – to Ezra’s surprise – and she took it as a signal to continue.

 

“That I had a good reason for it… and I had for 4 whole years. It took me a week to realise that she was talking about my uncertainty, not Smith.” Neo could hear a mocking tone and recognised it as a coping mechanism: _she makes fun of herself to get rid of the feeling that she failed, but at what?_

“Uncertainty?”

“I didn’t know if I could bring you back without complicating things for Zion. The Machines commanded that I bring you back and get rid of Smith within the week." Ezra's voice deepened, giving Neo the idea that she was angry with the Machines or - more than likely - herself.

"The week I was promised finished today.”

“What do you mean by 'bring me back'? And why would the machines have a problem with it?”

“Another question I can’t answer right now.” Ezra looked to her right for a second, seeing a police car with its red and blue lights flashing rhythmically. _But I'm not speeding!_ As the heavily tinted window came down, she let her mouth drop slightly in both shock and anger.

 

Ezra turned her head to the road ahead of them and sped up. The car, along with its driver, went a little faster to keep them beside him. Driving at 110 kilometres an hour on a motorbike was far more dangerous than using a car in her opinion: the car’s engine wouldn’t overheat from the strain of maintaining such a high speed and a car wouldn’t spin out of control if the wind picked up. Without warning, Ezra swerved in front of the car and turned to Neo, hoping that Smith wouldn’t overhear her instructions.

“Take the controls when I get up and keep us in front of the car, got it?” Ezra left him in the dark but it didn’t take him long to deduce what the girl had seen.

“How the hell did he get behind us?” Ezra could feel the clones, everywhere throughout the Matrix and gave Neo a three-word sentence that made his blood run cold. His concealed anger toward the ex-agent fuelled her desire to crush Smith like a bug beneath her boots tenfold.

“ **He** is everywhere.” The venom in her voice made him feel like shuddering, but Neo held back. Showing Ezra or Smith his weaknesses was the worst thing he could possibly do.

 

“Are you ready?” Neo said and did nothing, so Ezra took it as his strict concentration, his entire body slowly moving forward. As Ezra’s rather large feet left the brake pedal, Neo slipped his feet below hers, slowly replacing her hands on the bars with his own. Ezra’s hands moved inward as she manipulated the code, making her body as light as the air around her. She sat on the seat in a side-saddle fashion and moved her body upward into the air, doing a handstand while Neo drove his hips forward and took complete control over the motorbike. Using momentum to her advantage, Ezra pulled her chest down to the bars and catapulted over to the roof of the police car behind them as Smith drew out a gun, allowing her body to return to it's normal weight. Another fire fight was about to begin on the Freeway.

 

I have now learnt not to make any promises when it comes to chapter writing: I have 2 other fics that require attention to detail and this one is the most tasking as I try to include references and information from the original movie trilogy, so bear with me on this! (I also beg that you check the other's out if you want, because 1 of them needs suggestions from users)


	5. We're Not Built of Steel

**Summary for the Chapter:**

> Ezra (with Neo's help) takes out Smith and takes him to the orphanage, but what will happen when Neo falls into unconsciousness?

Smith fired a barrage of bullets into the roof of the police car, listening for any possible movement that might come from the girl above him. When he heard a loud bang above his head, Smith waited for the sound of something hitting the road to confirm his suspicions, but there was none. Ezra was out of harm’s way, her right leg on the window frame of the police car’s rear window which had been left wide open. She was holding onto a handle inside the car’s front window, thankful to whatever God guarded humanity that Smith hadn’t noticed it… yet. The ex-agent saw something in his peripheral vision, but it was far too late to stop the inevitable. Ezra swung her legs around, with her entire body’s momentum behind them, into the car. One foot hit Smith’s face and knock him out. Grabbing onto the driver’s shoulder as they veered toward the concrete dividers, Ezra watched the body become brighter and brighter until a film of code shattered like glass, revealing a very shocked and surprisingly living undercover policeman. Ezra ducked out through the window and got back onto the roof, leaping out in front of the car - now back in the middle lane - to the motorbike where Neo was waiting for her.

 

It swerved a little but Neo quickly gained control, the feeling two hands on his ribs confirming that Ezra’s escape had been the cause.

“Take the next left onto the open road. Don’t let anybody cut us off.” Neo nodded and looked around as he made the turn, noticing a small dirt road that he had never noticed before. Ezra hadn’t said anything but he knew he needed to go that way, the feeling growing so strong that he had no choice. It wasn’t until Ezra laughed into her hand that Neo realised what he’d done.

“Should I have gone straight?” The girl shook her head with the traces of a smile on her face.

“You’ll have to forgive me, but I never thought you would be so well attuned to the hardline.”

Neo shook his head and smiled; something he rarely did when others people were around.

“How many things have changed in the Matrix since I left?” Ezra gave him a smile of admiration and minor amusement. _I think he could use the humour… there will be so much to take in._

“Everything.” Ezra kept her eyes glued to the road which had become dustier, with a few derelict houses around them with large gap in between.

 

The few trees around were just as barren as the landscape with a handful of leaves on the wiry branches. When they were a little less than 500 metres from the end of the dirt-covered road, she politely ordered Neo to stop. Needless to say, his question went unnoticed by Ezra, who was eager to show him what she was capable of. _He doubts me too much… but I’ve proven where my loyalties lie, isn’t that enough?_

“Where’s the orphanage you spoke about?” The girl swung her leg over the seat and dismounted with what little grace she had left in her body, Neo doing the same when she was out of his way. Her words sent a little shiver up his spine; she sounded as though she was about to murder him, an act he had considered impossible for someone of her age.

“Wait and see.” Ezra walked out in front of the motorbike so that Neo could see what she was about to do, hoping it might make him fear her a little, or at least respect her more than she seemed to. In one swift, graceful motion, Ezra’s left leg moved out if front of her body, her second following through as her right arm swung around, right leg and arm meeting the ground a split second apart.

 

From her kneeling form a green light flashed out across the road in a perfectly straight line. As she stood up, Neo suddenly fell against the motorbike and nearly blacked out. He felt tired, hungry and drained of what energy was left in his body. Ezra felt it and was by his side in a moment.

“Your body in the real world is drained of nutrients and your mind is no better. We have to get you down there.” Ezra quickly pointed to the green line, the end closest to them lowering down like a ramp to a tunnel and them putting her hand back under his arms. _He doesn’t need to hear the details of his coming to be here, not yet. He needs time to heal physically… Only then can he heal mentally, surrounded by those who love him and know him better than I do._ Fluorescent lights flickered on, lighting up an underground tunnel. The ‘ramp’ hit the floor with a loud crack as some of the soil fell from its open edges, creaking under the pressure. Ezra helped Neo back onto the motorbike and drove down the ramp, through the tunnel. She was too eager to help him, but eagerness could have cost them their lives. When they were less than 100 metres from the wall at the end of the tunnel, she put on the breaks, the smell of burning rubber filling their noses.

 

The motorbike stopped less than a ruler’s length from the wall, secretly rocking Neo to the core. _Am I really that important to her that she would risk both of our deaths?_ His last conscious thought was where he could possibly be, but he didn’t have the chance to ask. As Ezra turned to ask Neo if he was okay, he tried to stand, but instead collapsed in a heap, the motorbike falling onto his legs. With a raised hand, Ezra made the motorbike lift into the air, freeing Neo’s legs. All she had to do was hide him from view so that he could return to the real world. Using a black sheet, she stood the motorbike back up beside Neo so that he was behind it and flung the sheet over him. Ezra stood and stared down at Neo, keeping an eye on his lack of movement. _His heart is still beating._

“Activate hardline. Requesting Subject Transfer from Matrix Simulation.” A voice came into Ezra’s head, as if it were her own thoughts talking back to her.

 _“Which subject?”_ Ezra thought for a moment, remembering what would happen if she gave the wrong name to the computer. _If he leaves first then I’ll have to instruct him from inside the Matrix… it was like a week in hell._

 

“Subject name: Ezra. Classification Status: Urgent.”

 _“Please identify yourself.”_ Ezra sighed and looked at the wall opposite her, leaning more on one leg than the other. _Maybe I need to find a way to confirm who I am without all these protocols… but that would mean going against the Council’s wishes._ Her voice became hilariously monotone, but nobody was there to laugh.

“Subject name: Ezra, passcode two, two, zero, zero.” A whirring sound echoed through Ezra’s ears as the computer registered her passcode, her highly-likely date of birth.

 _“Passcode Status: Accepted. Subject Transfer from Matrix Simulation: Accepted. Please relax as you are transferred from the Matrix Simulation.”_ Ezra smiled as her body broke up into pieces of code and faded away, leaving Neo’s unconscious body all alone.

_When he wakes up, he’ll get the biggest surprise of his life._

 

 

Sorry to make this a long wait but life got in the way :D

I hope to put up a few more over the holidays, so keep an eye out. Big shout out to my newest hits! To others who want to show their enjoyment of my work is welcome in the form of comments or kudos.

(You don't have to if you don't want to, I understand that people are busy in their personal lives). 


	6. Our Last Hope Part 1

**Summary for the Chapter:**

> Neo wakes up and scrapes up the beginnings of a woeful tale that his friends have been living through for over a decade...

Neo’s vision was shrouded in darkness, a piece of cloth tied around his eyes. The most important but irrelevant question of his location plagued his mind, but he didn’t dare move. Whatever had happened in the Matrix, he could see or hear –

“Neo… are you awake?” He turned his head and saw the outline of the teenage girl, moving his arms to no avail. They had been held down by steel cuffs, his ankles in the same predicament.

“Why am I being held prisoner?” Ezra laughed, starting out quietly and ending on an almost hysterical squeal. Neo was confused and terrified: _what’s going on?_ Ezra began to press button on a panel by Neo’s head and a large object slid from the depths of his skull, the sensation sending a shiver down his spine. The metal clasps released with a soft click and he sat upright, as if Ezra had stuck him with a pin, pulling the blindfold from his eyes. He was surprised to find that he could see in black and white, colour slowly fading in as the eyes adjusted to the programming inside of them. Ezra was smiling at him from a small panel by his head, his entire upper body twisted in the young lady’s direction.

“What happened to my eyes?” Ezra’s smiled dropped and she glared at him, completely unimpressed at not being thanked for giving the man his sight back.

 

She got up in his face and he couldn’t help but admit to himself that she was beginning to scare him.

“I’ll turn them off if you like… then you’ll be in total darkness with nobody but me for company. What was it that you were saying?” Neo stared her down, the girl taking the anger in his artificial eyes as a hint to back off. Ezra handed Neo a mirror and he slowly lifted it up, a few scars along his brow and around the sides of his nose. _She couldn’t have done this… it’s too advanced for someone her age to…_ Neo cut himself off, remembering what she could do in the Matrix. With skills like that, how could he say that it was completely impossible? He looked at Ezra again, noting her clothes in fine detail. His eyes caught onto the deep green of her long flowing gown, the red undercoat likening her to a rosebud before it had bloomed. The red sash around her waist ruined the illusion in his mind, finding her strangely beautiful despite himself. Around her shoulders hung a hooded black cloak that blended in with her hair, the thick wavy locks kept far from her face. Ezra could feel his eyes ogling her clothes and she could see that an explanation was needed.

“We have to see the Council and they mustn’t know who I am until they’ve seen you alive and well. I have some clothing here for you, so change quickly. If too many people spot me they’ll tell the Council and you may not be able to use those new eyes I made for much longer.”

 

Ezra sighed and picked up a pile of clothes form the bed across from Neo, his eyes hovering about the room. The sheer size of it was terrifying – row after row of the same lightly padded bed laid out in prefect symmetry – so uniform and dull. Ignoring the clothes, Neo looked straight ahead and saw that he was on the first row near the door, four more beds ahead and five behind, all with familiar spikes hanging underneath a hole in the bed where someone’s head had or would soon be. To his right, directly across from his bed was a door with a metal frame, the wall to the left of it covered in screens bordered by black and filled with a red-pink background. Wanting to closer investigate, Neo threw his legs over the side of the bed and walked over to the screens, finally realising what he had been looking at: on almost every screen was a boy or girl moving about while still integrated into the Matrix by their ‘natural’ connections. The screen only displayed their bodies from the neck upward, likely for privacy, which he understood completely. Neo was amazingly aware of how young they were, the oldest a couple of years younger than Ezra by his own estimations.

“Who are they?” Ezra craned her head to look at the bodies around them, noticing only of the screens that had been switched off.

“Our last hope.”


	7. Our Last Hope Part 2

**Summary for the Chapter:**

> Neo wants Ezra to answer the questions that he has, but the manner he uses doesn't impress her at all.

Neo stared at Ezra as she eyed a blank screen, tears forming in her eyes. He felt a draft in the air and realised that his clothes were the same tattered shirt and pair of pants that he’d died in, stains across his chest where mucus and blood had spattered when Bane – then possessed by Smith – had electrified his eyes and left them burn craters in his face. He glanced between Ezra and the screen, another stupidly insensitive question coming to mind.

“What do the blank screens and ‘our last hope’ mean?” Ezra dropped some pants and a t-shirt onto a bed behind him, her voice monotone with hints of sadness that he easily picked up on.

“Get dressed and knock on the door when you’re ready to leave. I’ll answer all your questions as soon as I regain my composure.” Ezra had delivered the entire sentence without making eye contact and swiftly left the room, leaving Neo behind with the clothes and his own thoughts.

 

The moment he undressed himself, he saw scars across his chest, stomach and one that ran down his back – having looked at himself in one of the black screens – realising how much of his muscle and fat had worn away. Now he was literally a shell of his former self, covered in battle wounds that had healed thanks to someone he would never get to thank. The red long-sleeved shirt, dark blue pants and black boots – which he’d found sitting under the bed – were nothing special, but they were so comfortable he could hardly believe they’d come from Zion. Neo walked to the door and knocked lightly, opening it with the press of a button when Ezra said nothing. _How did someone automate the doors? Usually you need to turn a wheel or pull a handle but now all I have to do is press a button? This kind of technology could change… everything._ Neo looked back as the door slid open, realising that whoever had changed the doors in this building had also changed the way humans accessed the Matrix.

 

That person was who he needed to talk to, not the little girl who was upset over a black screen on a wall.

“Who made all of this?” Ezra tilted her head slightly and looked him in the eyes, a grin on her face.

“Who do you think?” Neo glared at her, his steely expression becoming rage.

“I want ANSWERS! All I ever got in the Matrix was riddle after riddle but now I need answers! Can’t you get that through your pre-pubescent skull?!” Ezra had a similar look of contempt on her face, nostrils flared and teeth clench tightly together until she spoke.

“If you want to know ask politely and I’ll consider it! I brought you back from the dead and you repay me with nothing but insults and careless thoughts; does that seem fair to you at all?” Ezra had gradually transformed, losing the anger and questioning his with her raised eyebrows and an inquisitive expression.

 

Knowing how much his shouting was uncalled for, Neo lowered his voice and found his gaze locked with hers, pleading with her to help him silently.

“I don’t know where anyone is, where I am or why I’ve been brought back by you; as odd as it may sound I’m scared that nobody who knew me will be alive.” Ezra sighed and looked to the floor, passing Neo a black cloak. The hint of a smile in her face provided him some small comfort.

“Come with me and I promise I’ll tell you everything: stress isn’t going to do you any good, especially when you’re in this condition. Your first priority should be eating something.”

“Tell me something on the way there.” Ezra smiled and put her hands in the air, surrendering to the look in his eye that said he was desperate to hear something of the world now.

“Fine you win: put on the cloak and I’ll explain all those screens. It’s freezing out here.” Feeling the cold creep through his clothing, Neo threw the cloak over himself and followed Ezra through corridors and walkways until they reached a pair of metal doors. Ezra pressed a green button by the door and it opened, the red one next to it standing out like a sore thumb. Another question he wanted answered; another question that would have to wait.

 

Just like you, because I need time to develop the storyline from here: hope you’ve enjoyed reading this story so far!    


	8. Blank Screens Are Bad

**Summary for the Chapter:**

> Neo asks questions as Ezra allows him into another part of her life, finally finding out what the blank screens and other parts of this strange facility do.  
> There are even more questions that stem from the placement of the once-mighty Zion.

Neo watched the doors swing open and he was greeted with a peculiar sighs: cube-shaped slabs of metal served as crude tables, each with four chairs at its four sides. They were twisted and had multiple metallic colours on them, some more copper than others. A few had gold or lapis flecks in them and it only piqued his curiosity: how many more questions would pile up before they sat down? As if hearing Neo’s mind working hard to keep his thoughts in check, Ezra paused and gestured widely to the room.

“Take a seat. I’ll come back soon.” Ezra continued on her way and Neo sat in a chair to his right, finding it wholly uncomfortable but better than sitting on the floor. The young woman disappeared through a pair of metal doors at the end of the tall room, her cloak almost catching in the door. Ezra yanked at it and the cloth disappeared before the door shut on it, earning a flash of a grin from Neo.

 

She may try to be graceful and domineering, but she was still a child at heart. She was still vulnerable to life’s ups and downs like any other human on Earth. Ezra returned quickly with two red apples, shining one on her green sleeves. When she got to the table Ezra passed it to Neo and he took it graciously, thanking her before taking a small bite. It was crisp, sweet, just like the food in the Matrix. He wasn’t used to it. Neo’s mouth twitched as he continued chewing the hard flesh, his expression becoming a little softer than his steely – and very unnatural – blank gaze.

“So you want to know about the screens then?” Neo swallowed his first bite of the apple as Ezra took a bite of her own, nodding once as their eyes locked on one another. Ezra swallowed her apple after chewing it thoroughly, careful not to appear as famished as Neo.

“Those screens show all the children under my protection in the orphanage as they are in the real world: held prisoner by the Machines. Understood me so far?”

 

“I’m not a child Ezra. Anybody could understand what you’d just said.” Neo took an average sized chunk of apple in his mouth, the crunching sound it made almost deafening. He couldn’t hide his embarrassment but **God** did it taste better than the flavourless mush they served on the ships. Ezra said nothing, hints of laughter in her eyes and the small curl at the corner of her lips.

“Forgive me if you can Neo. I’m used to talking to children as young as five all day long, not grown men.” Neo said nothing and she continued with the story, eyes falling to the table between them. The further through her story she got, the more Ezra wished she had done something differently, but she couldn’t change the past. She could only make plans for the future.

“The Machines have grown aggressive since your death and found out about my wanting to bring you back. As a sign that they were unwilling to keep your promise they went on a rampage for a whole twenty seconds: they killed a handful of children in front of the Council the very day I started up the cameras.

 

“They smashed the pods open and cut into them…” Ezra’s eyes watered and Neo almost choked on his apple. _Was that why she cried earlier? Because they died in front of her?_

“On a couple of the screens we could see blood, limbs from other children’s bodies; they were massacred in seconds out of rage. I had to shut off the cameras because nobody was in there to watch out for.” Ezra looked up and saw Neo’s eyes fill with an emotion she’d not expected to see, even in such a small amount. Sympathy.

“I lost someone too.” Ezra let her face relax, sadness seeping into her mind and clouding her judgement. Her tears began to fade almost immediately.

“I couldn’t save her no matter how much I wanted to. Don’t think you’re the only one.” Judgement was no longer in Ezra’s vocabulary. All she heard was the Council’s words and the anger she’d felt.

“Do you know what their deaths cost me?” Now anger was taking over, overturning the sadness.

 

“Not only was I powerless to stop what happened, but the Council blamed me for it. They pushed their hatred of the Machine’s actions onto a ten year old girl and denied me access to the city. Those selfish idiots think I’m in cahoots with the Machines and Smith. You will go with me to Zion so I can get the parts for your bionic eyes and to prove once and for all that I would **never** help that bastard.” Ezra stood and left, fast-walking through the double doors. Neo left his apple on the table and followed after her in a hurry. Neo forced his way through the doors and found a small cave, a second and far larger one tapering off to his left. Inside the bigger of the two caves (which served as a hangar) was a single, solitary ship. At best it was half the size of the Nebuchadnezzar, if not smaller. In front of him Ezra was packing a small drawstring bag with 2 metal canteens water and a glass screen. Judging by the small knobs, buttons and array of metal fixtures along one of the shorter edges, it was going to be used to display some kind of image.

 

“Are you?” Ezra’s head snapped in Neo’s direction as she tightened the straps of the fabric bag, the fury in her face scaring him a little. Her mood swings should have given her whiplash by now.

“Am I **what**?” she half whispered and half spat at him.

“Working with the Machines.” Ezra sighed and pressed a green button of the rock above the bench she’d been preparing the bag on. A tall gate at the end of the room screeched as it moved upward into the rock of the cave, a few stones coming loose and hitting the floor. Light filtered into the cave and Neo ignored Ezra, walking to the gate. His eyes followed a rocky path to four thin metal rods holding up a wooden slab. In a few seconds he realised that it was an elevator, seeing the lever fixed on the rock around the ceiling of a giant cave. Zion was no longer the place he remembered it to be.      


	9. Returning to Zion Part 1

**Summary for the Chapter:**

> I really doubt that I need to explain what's happening here: the title says it all.

Neo was staring in awe at the large city below built in the shape of a tree, likely through the meticulous planning of a mad genius. On the lower levels of the tree were stalls with small metal plated houses scattered around and between them albeit there was plenty of space to move around in. Further up the cave wall was another level covered over in brass that shone in the artificial light hung around the massive cave, likely a place for the Zion Council to meet. Ezra was standing to his left with the bag and stared at him until he looked over to her.

 

“You’re going to need this,” she said, holding the canteen out to Neo.

He took it from her outstretched hand and looked back down at the city, noticing a niche carved into the rock above the various ‘branches’ of the city, likely to be places of residence. Neo could not however, scratch out the idea that they were control rooms full of men and women who were running the docking bays or giving commands to ships… but where were they?

“If you have another question I’m sure I can give you the answers you need Neo,” Ezra said with a cool tone, “but don’t expect too many big words in my sentences like everybody else you’ve met. I’m a teenager not an encyclopaedia.”

 

Neo thought to smirk, but only gave her a confused glare and then raised an eyebrow.

“Is there a difference?” he asked jokingly.

Ezra chuckled and walked past him, heading down a cut-out walkway in the rock of the cave as she made her way over to the makeshift elevator. Neo was walking behind her, glancing at the new city if Zion every few seconds to be sure that it was real and not a dream.

“You ever been on anything like this before?” she asked loudly, breaking Neo from his concentrated stare.

 

He glanced at the level on the wall and the elevator; a thick slab of metal with heavy-duty fastenings and a definitely-home-made pulley system – he wouldn’t get to Zion without dying for sure.

“I promise you that it’s completely safe.” Ezra announced as if hearing his thoughts, “I did build that eye and the hydraulics for that door.”

Ezra threw a thumb over her shoulder and pointed it at the door they had walked through to get into the giant chamber.

 

“I also helped rebuild Zion,” she boasted with hints of a smile turning up the corners of her lips.

“But you’re just a kid… you can’t build complicated machines,” Neo said in a stern tone.

Ezra was quick to defend herself.

“And you were just a man who couldn’t possibly defeat the Machines,” she pointed out, “that makes us two idiots who made the right mistakes.”

Neo was tempted to slap the cheeky grin off of the young woman’s face but he knew it wouldn’t do him any good. She was just trying to have fun.

 

 

I know this is an unusually short chapter, but I have an excess of four other fics to write and remember plot lines for, so apologies if my writing lacks its usual quality or imagination - school is a pain BTW


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